#include "needlemanoverlap.hpp"
#include "trimoligos.h"
+
//**********************************************************************************************************************
vector<string> TrimSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
CommandParameter pmaxhomop("maxhomop", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxhomop);
string helpString = "";
helpString += "The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.\n";
helpString += "The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.\n";
- helpString += "The trim.seqs command parameters are fasta, name, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n";
+ helpString += "The trim.seqs command parameters are fasta, name, count, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n";
helpString += "The fasta parameter is required.\n";
helpString += "The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n";
helpString += "The oligos parameter allows you to provide an oligos file.\n";
helpString += "The name parameter allows you to provide a names file with your fasta file.\n";
+ helpString += "The count parameter allows you to provide a count file with your fasta file.\n";
helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
else if (type == "fasta") { outputFileName = "fasta"; }
else if (type == "group") { outputFileName = "groups"; }
else if (type == "name") { outputFileName = "names"; }
+ else if (type == "count") { outputFileName = "count_table"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
}
return outputFileName;
outputTypes["qfile"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
outputTypes["qfile"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
}
if (temp == "not found") { nameFile = ""; }
else if(temp == "not open") { nameFile = ""; abort = true; }
else { nameFile = temp; m->setNameFile(nameFile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((countfile != "") && (nameFile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
m->mothurConvert(temp, qThreshold);
abort = true;
}
- if (nameFile == "") {
- vector<string> files; files.push_back(fastaFile);
- parser.getNameFile(files);
- }
+ if (countfile == "") {
+ if (nameFile == "") {
+ vector<string> files; files.push_back(fastaFile);
+ parser.getNameFile(files);
+ }
+ }
}
}
outputTypes["name"].push_back(trimNameFile);
outputTypes["name"].push_back(scrapNameFile);
}
+
+ string trimCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + "trim." + getOutputFileNameTag("count");
+ string scrapCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + "scrap." + getOutputFileNameTag("count");
+
+ if (countfile != "") {
+ CountTable ct;
+ ct.readTable(countfile);
+ nameCount = ct.getNameMap();
+ outputNames.push_back(trimCountFile);
+ outputNames.push_back(scrapCountFile);
+ outputTypes["count"].push_back(trimCountFile);
+ outputTypes["count"].push_back(scrapCountFile);
+ }
+
if (m->control_pressed) { return 0; }
string outputGroupFileName;
if(oligoFile != ""){
createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
- if (createGroup) {
+ if ((createGroup) && (countfile == "")){
outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + getOutputFileNameTag("group");
outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
}
setLines(fastaFile, qFileName);
if(processors == 1){
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, trimCountFile, scrapCountFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
}else{
- createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames);
+ createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, trimCountFile, scrapCountFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames);
}
for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
outputNames = outputNames2;
- for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
- ifstream in;
- m->openInputFile(it->first, in);
-
- ofstream out;
- string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first)) + getOutputFileNameTag("group");
- outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
- m->openOutputFile(thisGroupName, out);
-
- while (!in.eof()){
- if (m->control_pressed) { break; }
-
- Sequence currSeq(in); m->gobble(in);
- out << currSeq.getName() << '\t' << it->second << endl;
+ for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
+ ifstream in;
+ m->openInputFile(it->first, in);
+
+ ofstream out;
+ string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first));
+ if (countfile == "") { thisGroupName += getOutputFileNameTag("group"); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); }
+ else { thisGroupName += getOutputFileNameTag("count"); outputNames.push_back(thisGroupName); outputTypes["count"].push_back(thisGroupName); }
+ m->openOutputFile(thisGroupName, out);
+
+ if (countfile != "") { out << "Representative_Sequence\ttotal\t" << it->second << endl; }
+
+ while (!in.eof()){
+ if (m->control_pressed) { break; }
- if (nameFile != "") {
- map<string, string>::iterator itName = nameMap.find(currSeq.getName());
- if (itName != nameMap.end()) {
- vector<string> thisSeqsNames;
- m->splitAtChar(itName->second, thisSeqsNames, ',');
- for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
- out << thisSeqsNames[k] << '\t' << it->second << endl;
- }
- }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ Sequence currSeq(in); m->gobble(in);
+ if (countfile == "") {
+ out << currSeq.getName() << '\t' << it->second << endl;
+
+ if (nameFile != "") {
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) {
+ vector<string> thisSeqsNames;
+ m->splitAtChar(itName->second, thisSeqsNames, ',');
+ for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+ out << thisSeqsNames[k] << '\t' << it->second << endl;
+ }
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
+ }else {
+ map<string, int>::iterator itTotalReps = nameCount.find(currSeq.getName());
+ if (itTotalReps != nameCount.end()) { out << currSeq.getName() << '\t' << itTotalReps->second << '\t' << itTotalReps->second << endl; }
+ else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
}
- }
- in.close();
- out.close();
- }
+ }
+ in.close();
+ out.close();
+ }
+
+ if (countfile != "") { //create countfile with group info included
+ CountTable* ct = new CountTable();
+ ct->readTable(trimCountFile);
+ map<string, int> justTrimmedNames = ct->getNameMap();
+ delete ct;
+
+ CountTable newCt;
+ for (map<string, int>::iterator itCount = groupCounts.begin(); itCount != groupCounts.end(); itCount++) { newCt.addGroup(itCount->first); }
+ vector<int> tempCounts; tempCounts.resize(groupCounts.size(), 0);
+ for (map<string, int>::iterator itNames = justTrimmedNames.begin(); itNames != justTrimmedNames.end(); itNames++) {
+ newCt.push_back(itNames->first, tempCounts); //add it to the table with no abundance so we can set the groups abundance
+ map<string, string>::iterator it2 = groupMap.find(itNames->first);
+ if (it2 != groupMap.end()) { newCt.setAbund(itNames->first, it2->second, itNames->second); }
+ else { m->mothurOut("[ERROR]: missing group info for " + itNames->first + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ }
+ newCt.printTable(trimCountFile);
+ }
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
/**************************************************************************************/
-
-int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string trimNFileName, string scrapNFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames, linePair line, linePair qline) {
+int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string trimNFileName, string scrapNFileName, string trimCFileName, string scrapCFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames, linePair line, linePair qline) {
try {
m->openOutputFile(scrapNFileName, scrapNameFile);
}
+ ofstream trimCountFile;
+ ofstream scrapCountFile;
+ if(countfile != ""){
+ m->openOutputFile(trimCFileName, trimCountFile);
+ m->openOutputFile(scrapCFileName, scrapCountFile);
+ if (line.start == 0) { trimCountFile << "Representative_Sequence\ttotal" << endl; scrapCountFile << "Representative_Sequence\ttotal" << endl; }
+ }
ofstream outGroupsFile;
- if (createGroup){ m->openOutputFile(groupFileName, outGroupsFile); }
+ if ((createGroup) && (countfile == "")){ m->openOutputFile(groupFileName, outGroupsFile); }
if(allFiles){
for (int i = 0; i < fastaFileNames.size(); i++) { //clears old file
for (int j = 0; j < fastaFileNames[i].size(); j++) { //clears old file
int count = 0;
bool moreSeqs = 1;
- TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer);
+ TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
while (moreSeqs) {
if (m->control_pressed) {
inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
- if (createGroup) { outGroupsFile.close(); }
-
- if(qFileName != ""){
- qFile.close();
- }
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
-
- return 0;
+ if ((createGroup) && (countfile == "")) { outGroupsFile.close(); }
+ if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
+ if(nameFile != "") { scrapNameFile.close(); trimNameFile.close(); }
+ if(countfile != "") { scrapCountFile.close(); trimCountFile.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0;
}
int success = 1;
if(success > bdiffs) { trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
-
- if(rbarcodes.size() != 0){
- success = trimOligos.stripRBarcode(currSeq, currQual, barcodeIndex);
- if(success > bdiffs) { trashCode += 'b'; }
- else{ currentSeqsDiffs += success; }
- }
if(numSpacers != 0){
success = trimOligos.stripSpacer(currSeq, currQual);
}
}
+ if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + ", trashcode= " + trashCode); if (trashCode.length() != 0) { m->mothurOutEndLine(); } }
+
if(trashCode.length() == 0){
currSeq.setAligned(currSeq.getUnaligned());
currSeq.printSequence(trimFASTAFile);
if (itName != nameMap.end()) { trimNameFile << itName->first << '\t' << itName->second << endl; }
else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
}
+
+ int numRedundants = 0;
+ if (countfile != "") {
+ map<string, int>::iterator itCount = nameCount.find(currSeq.getName());
+ if (itCount != nameCount.end()) {
+ trimCountFile << itCount->first << '\t' << itCount->second << endl;
+ numRedundants = itCount->second-1;
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
+ }
if (createGroup) {
if(barcodes.size() != 0){
}
}
- outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
+ if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
+
+ if (countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
+ else { groupMap[currSeq.getName()] = thisGroup; }
- int numRedundants = 0;
if (nameFile != "") {
map<string, string>::iterator itName = nameMap.find(currSeq.getName());
if (itName != nameMap.end()) {
if (itName != nameMap.end()) { scrapNameFile << itName->first << '\t' << itName->second << endl; }
else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
}
+ if (countfile != "") {
+ map<string, int>::iterator itCount = nameCount.find(currSeq.getName());
+ if (itCount != nameCount.end()) {
+ trimCountFile << itCount->first << '\t' << itCount->second << endl;
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
+ }
+
currSeq.setName(currSeq.getName() + '|' + trashCode);
currSeq.setUnaligned(origSeq);
currSeq.setAligned(origSeq);
if (createGroup) { outGroupsFile.close(); }
if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
if(nameFile != "") { scrapNameFile.close(); trimNameFile.close(); }
+ if(countfile != "") { scrapCountFile.close(); trimCountFile.close(); }
return count;
}
/**************************************************************************************************/
-int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
+int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string trimCountFileName, string scrapCountFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
try {
int process = 1;
(scrapQualFileName + toString(getpid()) + ".temp"),
(trimNameFileName + toString(getpid()) + ".temp"),
(scrapNameFileName + toString(getpid()) + ".temp"),
+ (trimCountFileName + toString(getpid()) + ".temp"),
+ (scrapCountFileName + toString(getpid()) + ".temp"),
(groupFile + toString(getpid()) + ".temp"),
tempFASTAFileNames,
tempPrimerQualFileNames,
for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
out << it->first << '\t' << it->second << endl;
}
+
+ out << groupMap.size() << endl;
+ for (map<string, string>::iterator it = groupMap.begin(); it != groupMap.end(); it++) {
+ out << it->first << '\t' << it->second << endl;
+ }
out.close();
}
exit(0);
m->openOutputFile(trimNameFileName, temp); temp.close();
m->openOutputFile(scrapNameFileName, temp); temp.close();
}
+ if (countfile != "") {
+ m->openOutputFile(trimCountFileName, temp); temp.close();
+ m->openOutputFile(scrapCountFileName, temp); temp.close();
+ }
- driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
+ driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, trimCountFileName, scrapCountFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
HANDLE hThreadArray[processors-1];
//Create processor worker threads.
- for( int i=0; i<processors-1; i++){
+ for( int h=0; h<processors-1; h++){
string extension = "";
- if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
+ if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
vector<vector<string> > tempFASTAFileNames = fastaFileNames;
vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
vector<vector<string> > tempNameFileNames = nameFileNames;
trimData* tempTrim = new trimData(filename,
- qFileName, nameFile,
+ qFileName, nameFile, countfile,
(trimFASTAFileName+extension),
(scrapFASTAFileName+extension),
(trimQualFileName+extension),
(scrapQualFileName+extension),
(trimNameFileName+extension),
(scrapNameFileName+extension),
+ (trimCountFileName+extension),
+ (scrapCountFileName+extension),
(groupFile+extension),
tempFASTAFileNames,
tempPrimerQualFileNames,
tempNameFileNames,
- lines[i].start, lines[i].end, qLines[i].start, qLines[i].end, m,
- pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer,
+ lines[h].start, lines[h].end, qLines[h].start, qLines[h].end, m,
+ pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer,
primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
- minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap);
+ minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap, nameCount);
pDataArray.push_back(tempTrim);
- hThreadArray[i] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ hThreadArray[h] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
}
//parent do my part
m->openOutputFile(trimNameFileName, temp); temp.close();
m->openOutputFile(scrapNameFileName, temp); temp.close();
}
+ vector<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+ vector<vector<string> > tempNameFileNames = nameFileNames;
+ if(allFiles){
+ ofstream temp;
+ string extension = toString(processors-1) + ".temp";
+ for(int i=0;i<tempFASTAFileNames.size();i++){
+ for(int j=0;j<tempFASTAFileNames[i].size();j++){
+ if (tempFASTAFileNames[i][j] != "") {
+ tempFASTAFileNames[i][j] += extension;
+ m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
+
+ if(qFileName != ""){
+ tempPrimerQualFileNames[i][j] += extension;
+ m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
+ }
+ if(nameFile != ""){
+ tempNameFileNames[i][j] += extension;
+ m->openOutputFile(tempNameFileNames[i][j], temp); temp.close();
+ }
+ }
+ }
+ }
+ }
- driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), fastaFileNames, qualFileNames, nameFileNames, lines[processors-1], qLines[processors-1]);
+ driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (trimCountFileName + toString(processors-1) + ".temp"), (scrapCountFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames, tempNameFileNames, lines[processors-1], qLines[processors-1]);
processIDS.push_back(processors-1);
if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
else { groupCounts[it->first] += it->second; }
}
+ for (map<string, string>::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) {
+ map<string, string>::iterator it2 = groupMap.find(it->first);
+ if (it2 == groupMap.end()) { groupMap[it->first] = it->second; }
+ else { m->mothurOut("[ERROR]: " + it->first + " is in your fasta file more than once. Sequence names must be unique. please correct.\n"); }
+ }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
m->mothurRemove((scrapNameFileName + toString(processIDS[i]) + ".temp"));
}
+
+ if(countfile != ""){
+ m->appendFiles((trimCountFileName + toString(processIDS[i]) + ".temp"), trimCountFileName);
+ m->mothurRemove((trimCountFileName + toString(processIDS[i]) + ".temp"));
+ m->appendFiles((scrapCountFileName + toString(processIDS[i]) + ".temp"), scrapCountFileName);
+ m->mothurRemove((scrapCountFileName + toString(processIDS[i]) + ".temp"));
+ }
- if(createGroup){
+ if((createGroup)&&(countfile == "")){
m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
}
in >> tempNum; m->gobble(in);
if (tempNum != 0) {
- while (!in.eof()) {
- in >> group >> tempNum; m->gobble(in);
+ for (int i = 0; i < tempNum; i++) {
+ int groupNum;
+ in >> group >> groupNum; m->gobble(in);
map<string, int>::iterator it = groupCounts.find(group);
- if (it == groupCounts.end()) { groupCounts[group] = tempNum; }
- else { groupCounts[it->first] += tempNum; }
+ if (it == groupCounts.end()) { groupCounts[group] = groupNum; }
+ else { groupCounts[it->first] += groupNum; }
+ }
+ }
+ in >> tempNum; m->gobble(in);
+ if (tempNum != 0) {
+ for (int i = 0; i < tempNum; i++) {
+ string group, seqName;
+ in >> seqName >> group; m->gobble(in);
+
+ map<string, string>::iterator it = groupMap.find(seqName);
+ if (it == groupMap.end()) { groupMap[seqName] = group; }
+ else { m->mothurOut("[ERROR]: " + seqName + " is in your fasta file more than once. Sequence names must be unique. please correct.\n"); }
}
}
+
in.close(); m->mothurRemove(tempFile);
}
#endif
}
else if(type == "BARCODE"){
inOligos >> group;
-
- //barcode lines can look like BARCODE atgcatgc groupName - for 454 seqs
- //or BARCODE atgcatgc atgcatgc groupName - for illumina data that has forward and reverse info
- string temp = "";
- while (!inOligos.eof()) {
- char c = inOligos.get();
- if (c == 10 || c == 13){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- else { temp += c; }
- }
- //then this is illumina data with 4 columns
- if (temp != "") {
-
- for(int i=0;i<group.length();i++){
- group[i] = toupper(group[i]);
- if(group[i] == 'U') { group[i] = 'T'; }
- }
-
- if (m->debug) { m->mothurOut("[DEBUG]: reading reverse " + group + ", and group = " + temp + ".\n"); }
-
- string reverseBarcode = reverseOligo(group); //reverse barcode
- //check for repeat barcodes
- map<string, int>::iterator itBar = rbarcodes.find(reverseBarcode);
- if (itBar != rbarcodes.end()) { m->mothurOut("reverse barcode " + group + " is in your oligos file already."); m->mothurOutEndLine(); }
-
- group = temp;
- rbarcodes[reverseBarcode]=indexBarcode;
- }else { if (m->debug) { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); } }
-
//check for repeat barcodes
map<string, int>::iterator itBar = barcodes.find(oligo);
if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
-
+
barcodes[oligo]=indexBarcode; indexBarcode++;
barcodeNameVector.push_back(group);
}else if(type == "LINKER"){
string fastaFileName = "";
string qualFileName = "";
string nameFileName = "";
+ string countFileName = "";
if(primerName == ""){
comboGroupName = barcodeNameVector[itBar->second];
nameFileNames[itBar->second][itPrimer->second] = nameFileName;
m->openOutputFile(nameFileName, temp); temp.close();
}
-
}
}
}
projects / mothur.git / blobdiff